Trouble selecting correct object in viewport
You can also try changing the selection mode under User Preferences.  There are two options available now for selection.  


OpenGL Select
OpenGL Occlusion Queries


OpenGL Occlusion Queries is the newer, and faster method which seems to work better on AMD Radeon GPUS.



You can also use shift+b to draw-out a rectangular selection that will cause the view to zoom in on the selected location.   Picking objects tends to work better when you are zoomed in closer.  

shift+c will zoom out out to fit the scene.  Using these two shortcuts, you can quickly navigate to whatever object you would like to select and work on.